1NCL

THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction.

Giartosio, A.Erent, M.Cervoni, L.Morera, S.Janin, J.Konrad, M.Lascu, I.

(1996) J Biol Chem 271: 17845-17851

  • DOI: https://doi.org/10.1074/jbc.271.30.17845
  • Primary Citation of Related Structures:  
    1NCL

  • PubMed Abstract: 

    The eukaryotic nucleoside diphosphate (NDP) kinases are hexamers, while the bacterial NDP kinases are tetramers made of small, single domain subunits. These enzymes represent an ideal model for studying the effect of subunit interaction on protein stability. The thermostability of NDP kinases of each class was studied by differential scanning calorimetry and biochemical methods. The hexameric NDP kinase from Dictyostelium discoideum displays one single, irreversible differential scanning calorimetry peak (Tm 62 degrees C) over a broad protein concentration, indicating a single step denaturation. The thermal stability of the protein was increased by ADP. The P105G substitution, which affects a loop implicated in subunit contacts, yields a protein that reversibly dissociates to folded monomers at 38 degrees C before the irreversible denaturation occurs (Tm 47 degrees C). ADP delays the dissociation, but does not change the Tm. These data indicate a "coupling" of the quaternary structure with the tertiary structure in the wild-type, but not in the mutated protein. We describe the x-ray structure of the P105G mutant at 2.2-A resolution. It is very similar to that of the wild-type protein. Therefore, a minimal change in the structure leads to a dramatic change of protein thermostability. The NDP kinase from Escherichia coli behaves like the P105G mutant of the Dictyostelium NDP kinase. The detailed study of their thermostability is important, since biological effects of thermolabile NDP kinases have been described in several organisms.


  • Organizational Affiliation

    Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Center of Molecular Biology of C.N.R., Università degli Studi "La Sapienza, " 00185 Roma, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE KINASE150Dictyostelium discoideumMutation(s): 1 
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.3α = 90
b = 74.3β = 90
c = 105.3γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Other
  • Version 1.4: 2024-02-14
    Changes: Data collection